Identification of Porphyromonas gingivalis virulence polynucleotides for diagnosis, treatment, and monitoring of periodontal diseases

ABSTRACT

The invention provides compositions and methods for the detection of  Porphyromonas gingivalis  and for the treatment and prevention of diseases and infections caused by  P. gingivalis.

PRIORITY

This application is a divisional application f U.S. Ser. No. 10/915,002, filed on Aug. 10, 2004, which claims the benefit of U.S. provisional application Ser. No. 60/495,589 filed on Aug. 15, 2003, both of which are incorporated by reference herein in their entirety.

GOVERNMENT INTERESTS

This invention was made with Government support under Grant Number RO1 DE10994-01A2 awarded by the National Institutes of Health. The Government has certain rights in the invention.

TECHNICAL AREA OF THE INVENTION

This invention provides methods and compositions for the diagnosis, treatment, prevention, and amelioration of diseases and infections caused by Porphyromonas gingivalis (Pg).

BACKGROUND OF THE INVENTION

Porphyromonas gingivalis is an important etiologic agent of periodontal diseases. It is estimated that over 49,000,000 people in the United States have some form of periodontitis (Cutler et al., Trends Microbiol. 3:45 (1995)). Periodontitis occurs with higher frequency in patients with systemic disease such as diabetes mellitus, AIDS, leukemia, neutropenia, Crohn's disease, and Down's syndrome (Neville et al., Oral and Maxillofacial Pathology. Philadelphia: Saunders, 1995). Currently, standard microbiological tests for Pg detect only the presence of Pg in dental plaque, but do not specifically identify disease activity. For this reason, these tests have a low positive predictive value. Because Pg is normally found in plaque of even healthy individuals, the application of these tests is limited in their usefulness to those who present with certain clinical manifestations of disease. These include the following: 1) patients with advanced attachment loss and bone loss before the age of 25; 2) Patients, usually aged 25-35, with rapid destruction of attachment and bone in a relatively short period of time (rapidly progressive periodontitis); 3) patients who continue to lose attachment despite stringent treatment (refractory periodontitis); and 4) patients older than 35 who have a slow rate of attachment loss.

Diagnostic tests are needed in the art for other types of patients including, for example: 1) certain preadolescent children whose mothers have a history of periodontitis who are in need of tests that will determine if thy have acquired a predisposition for the disease, including, for example, Papillon-Lefevre syndrome (PLS), hypophosphatasia, neutropenias, leukocyte adhesion deficiency (LAD), Chediak-Higashi syndrome, Down's syndrome, leukemia, histiocytosis X, early-onset Type 1 diabetes, and acrodynia; 2) other preadolescent children who are less prone would also benefit from such a test since there are no other predictors or known risk factors; 3) adults already diagnosed or not yet diagnosed would benefit from knowing whether or not they have Pg present that are disease primed.

A national survey of the United States revealed a prevalence of localized juvenile periodontitis of 0.53% and of generalized juvenile periodontitis of 0.13%. Loe & Brown, J. Periodontol. 62:608-616 (1991). Findings from a number of studies corroborate the conclusion that early-onset disease is similar in other industrialized countries and is more frequent in developing countries. Loe & Brown, J. Periodontol. 62:608-616 (1991). In addition, certain types of adult periodontitis, which in general is a very common condition affecting over half of the adult population, are likely to be cased by Pg. In short, a good diagnostic for Pg induced periodontal disease could became a standard operating procedure for dental practitioners worldwide. In should be noted that Pg can also cause extra-oral diseases such as endocarditis, thyroid gland abscesses, urinary tract infections, brain abscesses, and vertebral osteomyelitis.

There are antibiotic, surgical, and mechanical therapies for the treatment of Pg induced periodontitis, but no means for prevention. Tetracycline has been widely used in the treatment of early-onset periodontitis. There remains a concern, however, of strains developing resistance to tetracycline as well as the possibility of overgrowth of other pathogenic microorganisms subgingivally. Given the incidence of these diseases, a safe vaccine for Pg is needed. A vaccine can be, for example, a multivalent vaccine. Control of periodontal disease is also very important in light of recent attention to the possible role of periodontal infections as risk factors for systemic disease (e.g., coronary heart disease).

No significant advances in the diagnosis, treatment or prevention of periodontal diseases have occurred in the past three decades since antibiotic regimens were adopted. DNA probe technology and immunoassay technology has been developed to identify the presence of Pg in dental plaque, but these technologies are unable to distinguish between the Pg that is normally part of the dental plaque community and Pg that is involved in an actual disease process. Consequently, those dentists who use these technologies recognize that they do not provide a “gold standard” for diagnosing disease activity.

Early diagnosis of periodontitis is highly desirable. Currently, diagnosis is made by X-ray analysis usually long after the onset of the disease and after considerable damage to the supporting bone and tissue has occurred. Tooth loss is the ultimate detrimental effect of destructive periodontal disease. Most people have Pg as a normal member of their dental plaque, but it usually does not cause disease. When Pg does cause disease the human host mounts an enormous response but it is inevitably futile presumably because it is directed against the wrong Pg antigens.

Prevention is much preferred in medicine to treatment. Currently, the prevalence and severity of early-onset periodontal diseases is addressed with a combination of mechanical plaque removal and a variety of systemic and topically applied antimicrobial agents aimed at selectively removing or inhibiting pathogenic bacteria. An effective vaccine against Pg would effectively reduce the use of antibiotics to control the destructive aspects of the early-onset periodontal diseases.

Compared to the number of different infectious diseases, there are relatively few reliable diagnostic tests and vaccines. In large part this is because pathogens regulate expression of their genes that are essential to the disease process: important environmental signals that normally cause the bacteria to turn on virulence genes during an infection are missing when they are grown in the laboratory. Consequently, many of the best targets for diagnostic and vaccine strategies remain unknown.

SUMMARY OF THE INVENTION

One embodiment of the invention provides an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354167-226, 228-261, and 263-354. The immunogenic polypeptide can be part of an isolated polypeptide which also comprises a heterologous polypeptide.

Another embodiment of the invention provides an isolated polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354.

Still another embodiment of the invention provides an isolated polynucleotide comprising a sequence that encodes an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354.

Even another embodiment of the invention provides an isolated polynucleotide comprising at least about 15 contiguous nucleic acids of a sequence selected from the group consisting of SEQ ID NOs:1-166, 227, and 262 and degenerate variants thereof.

Another embodiment of the invention provides an isolated polynucleotide comprising polynucleotide sequence of SEQ ID NOs:1-166, 227, and 262 and degenerate variants thereof. The polynucleotide can be operably linked to an expression control sequence. The polynucleotide can also be part of a heterologous polynucleotide. The polynucleotide can be in an expression vector and the expression vector can be in a host cell.

Still another embodiment of the invention provides an antibody, antibody fragment, or single-chain antibody that specifically binds to an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354. The antibody fragment can be selected from the group consisting of Fab, F(ab′)₂, Fab′ and Fab′-SH. The antibody can be a monoclonal antibody or a polyclonal antibody. The antibody, antibody fragment, or single-chain antibody can be present in a composition comprising a pharmaceutically acceptable carrier.

Yet another embodiment of the invention provides a method for treating or preventing a disease or infection caused by Porphyromonas gingivalis comprising administering to an animal an antibody, antibody fragment, or single-chain antibody of the invention, whereby a disease or infection caused by Porphyromonas gingivalis is treated or prevented. The disease can be localized prepubertal periodontitis, generalized prepubertal periodontitis, localized juvenile periodontitis, generalized juvenile periodontitis, rapidly progressive adult periodontitis, refractory adult periodontitis, endiocarditis, thyroid gland abscess, urinary tract infection, brain abscess and vertebral osteomyelitis.

Even another embodiment of the invention provides a composition comprising an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354 and a pharmaceutically acceptable carrier.

Another embodiment of the invention provides a method of eliciting an immune response in an animal comprising administering an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354 to an animal, wherein an immune response is elicited.

Still another embodiment of the invention provides a method of treating or preventing a disease or infection caused by Porphyromonas gingivalis comprising administering an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354 to an animal, wherein the disease is treated or prevented.

Yet another embodiment of the invention provides a composition comprising an isolated polynucleotide comprising a sequence that encodes an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354 and a pharmaceutically acceptable carrier. The polynucleotide can be in a plasmid.

Even another embodiment of the invention provides a method of eliciting an immune response in an animal comprising administering an isolated polynucleotide comprising a sequence that encodes an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354 to an animal, wherein an immune response is elicited.

Another embodiment of the invention provides a method of treating or preventing a disease or infection caused by Porphyromonas gingivalis comprising administering an isolated polynucleotide comprising a sequence that encodes an isolated immunogenic polypeptide comprising about at least 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354 to an animal, wherein the disease or infection is treated or prevented.

Still another embodiment of the invention provides a method of detecting the presence of a first Porphyromonas gingivalis polynucleotide in a test sample. The method comprises contacting a test sample suspected of containing the first polynucleotide with a second polynucleotide under hybridization conditions, wherein the second polynucleotide is an isolated polynucleotide comprising a sequence that encodes an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354. Hybridized first and second polynucleotide complexes are detected. The presence of a hybridized first and second polynucleotide complex indicates the presence of a first polynucleotide in the test sample.

Yet another embodiment of the invention provides a method of detecting the presence of a Porphyromonas gingivalis antibody in a test sample. The method comprises contacting a test sample with an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354, wherein the polypeptide specifically binds a Porphyromonas gingivalis antibody under conditions that allow formation of an immunocomplex between the antibody and the polypeptide. An immunocomplex is detected. Detection of the immunocomplex indicates the presence of a Porphyromonas gingivalis antibody in the test sample.

Even another embodiment of the invention provides a method of detecting the presence of Porphyromonas gingivalis or a Porphyromonas gingivalis polypeptide in a test sample. The method comprises contacting a test sample with an antibody, antibody fragment, or single-chain antibody of the invention that specifically binds Porphyromonas gingivalis or a Porphyromonas gingivalis polypeptide under conditions that allow formation of an immunocomplex between the antibody and the Porphyromonas gingivalis or the Porphyromonas gingivalis polypeptide. Immunocomplexes are detected. Detection of immunocomplexes indicates the presence of Porphyromonas gingivalis or a Porphyromonas gingivalis polypeptide in the test sample. The Porphyromonas gingivalis polypeptide can be expressed in vivo during infection of an animal.

Another embodiment of the invention provides a method for detecting Porphyromonas gingivalis infection in a subject. The method comprises obtaining a biological sample from the subject and contacting the biological sample with an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354 under conditions that allow formation of immunocomplexes between the polypeptide and Porphyromonas gingivalis antibodies present in the biological sample. The amount of immunocomplexes formed is detected. The amount of immunocomplexes detected is compared to a control sample. A higher amount of immunocomplexes in the biological sample than the control sample indicates a Porphyromonas gingivalis infection in the subject.

Still another embodiment of the invention provides a method for detecting Porphyromonas gingivalis in a subject. The method comprises obtaining a biological sample from the subject and contacting the biological sample with an antibody, antibody fragment or single-chain antibody of the invention under conditions that allow formation of immunocomplexes between the antibody, antibody fragment, or single-chain antibody and Porphyromonas gingivalis polypeptides present in the biological sample. The amount of immunocomplexes formed is detected and the amount of immunocomplexes detected is compared to a control sample. A higher amount of immunocomplexes in the biological sample than in the control sample indicates a Porphyromonas gingivalis infection in the subject.

Yet another embodiment of the invention provides a method for detecting Porphyromonas gingivalis in a subject. The method comprises obtaining a biological sample from the subject, contacting the biological sample with an isolated polynucleotide comprising a sequence that encodes an isolated immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354 under conditions that allow formation of a hybridized complex between the polynucleotide and Porphyromonas gingivalis polynucleotides present in the biological sample. The amount of hybridized complexes formed is detected. The amount of hybridized complexes detected is compared to a control sample. A higher amount of hybridized complexes in the biological sample than in the control sample indicates a Porphyromonas gingivalis infection in the subject.

Therefore, the invention provides compositions and methods for the detection of Porphyromonas gingivalis and for the prevention and treatment of diseases and infections caused by P. gingivalis.

DETAILED DESCRIPTION OF THE INVENTION Methods of Identification of Polynucleotides and Polypeptides

Methods for identifying nucleotide sequences that are important to a microorganism's ability to cause disease has been applied to Pg, the principal etiologic agent of periodontal diseases, including, for example, early-onset periodontitis including localized prepubertal periodontitis, generalized prepubertal periodontitis, localized juvenile periodontitis, generalized juvenile periodontitis, rapidly progressive adult periodontitis, and refractory adult periodontitis. Pg can also cause endocarditis, thyroid gland abscesses, urinary tract infections, brain abscesses and vertebral osteomyelitis.

The methods used to identify polynucleotide and polypeptide sequences of the invention are termed in vivo induced antigen technology (IVIAT) (see Handfield et al., Trends Microbiol. 336:336-339 (2000); WO 01/11081) and In Vivo Expression Technology (IVET) (see Mahan et al., Proc Natl Acad Sci USA 92: 669-673 (January 1995); Handfield et al., Infect Immun 68: 2359-2362 (April 2000); Rainey & Preston, Curr Opin Biotechnol 11: 440-444 (2000).

Briefly, IVIAT comprises obtaining a sample of antibodies against Pg antigens that are expressed by Pg in vivo and in vitro and adsorbing the antibodies with cells or cellular extracts of Pg that have been grown in vitro. An example of a sample of antibodies that can be used is sera from patients who have been or are infected with Pg. The unadsorbed antibodies are isolated and are used to probe an expression library of Pg DNA. Reactive clones are isolated and the cloned fragments sequenced.

IVIAT was used to identify polynucleotides of Pg that are expressed only when Pg is engaged in actually causing disease in animals, and in particular humans. Important environmental signals that normally cause Pg to turn on virulence genes during an infection are missing when the bacteria are grown in the laboratory. Therefore, many of the best targets for diagnostic and vaccine strategies were unknown. IVIAT methodology was used to identify polynucleotides that are specifically turned on during growth of Pg in a human host and not during routine laboratory growth. These polynucleotides and corresponding polypeptides and antibodies are useful in developing diagnostic tests for Pg to identify, for example, subjects who are in early stages of infection and for monitoring response to therapy, and for developing vaccines or treatments to prevent or treat diseases caused by Pg in susceptible animals.

In vivo expression technology (IVET) provides powerful genetic tools for identifying and studying bacterial genes that are induced during infection of an animal model of infection. IVET is designed as a promoter trap method whereby random genomic fragments are ligated in front of a promoterless reporter gene (conferring antibiotic resistance for instance). Reporter activity can then be used as an indication of transcriptional activity of the fused gene. IVET was first used to identify in vivo-induced (ivi) genes in a mammalian pathogen in 1993 (Mahan et al. Infect Agents Dis. 2:263-8, 1993). An IVET strategy used herein was based on the fact that Pg is unable to survive passage through an antibiotic-treated mouse after sub-cutaneous inoculation. This strategy allows one to specifically select for a Pg genomic fragment that contains a promoter of a gene that is normally turned on during infection in the mouse and which confers antibiotic resistance to Pg. Only fusions that were active during infection result in expression of the antibiotic resistance marker and allow survival and multiplication of the strain in the animal. Most such strains had fusions that were also active during in vitro growth, i.e. these strains had constitutively active gene fusions. However, the subset of strains containing IVI gene fusions could easily be identified by antibiotic screening of output colonies. Output strains that were antibiotic sensitive were said to contain gene promoters that were specifically active within the host environment, but not under laboratory growth of Pg. A limitation of the IVET approach with Pg is that it relied on a recognized animal model of infection as the basis for in vivo expression. This limitation was directly addressed with IVIAT.

Pg antigens identified by IVIAT and IVET have a high predictive value with regard to diseases caused by Pg, for example, periodontal diseases. Diagnostic tests for Pg can be useful in applications such as screening children whose mothers have a history of periodontitis to determine if the children have acquired a predisposition for the disease. Diseases known to be associated with periodontitis before puberty include Papillon-Lefevre syndrome (PLS), hypophosphatasia, neutropenias, leukocyte adhesion deficiency (LAD), Chediak-Higashi syndrome, Down's syndrome, leukemia, histiocytosis X, early-onset Type I diabetes, and acrodynia. Children with these diseases are candidates for Pg testing. Additionally, other preadolescent children who are less prone to periodontitis would benefit from a Pg diagnostic test since there are no other predictors or known risk factors.

Polypeptides

Isolated polypeptides of the invention can either be full-length polypeptides or fragments of polypeptides. For example, fragments of polypeptides of the invention can comprise at least about 5, 10, 25, 50, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 1,500, or 2,000 contiguous amino acids of polypeptides of the invention. Polypeptides of the invention comprise or consist essentially of those shown in SEQ ID NO:167-226, 228-261, and 263-354. These polypeptides will be referred to as “the polypeptide SEQ IDs.” Polypeptides of the invention were discovered using IVIAT or IVET techniques. The polypeptides are described in Table 2. Where a polypeptide demonstrated homology to a known open reading frame in an organism, the name of the open reading frame and function of the open reading frame is given. The basic and novel characteristics of polypeptides of the invention that consist essentially of SEQ ID NOs:167-226, 228-261, and 263-354 is that they comprise or consist essentially of the sequence shown in SEQ ID NOs:167-226, 228-261, and 263-354 and that they specifically bind to a Pg-specific antibody, antibody fragment, single-chain antibody or aptamer of the invention.

In one embodiment of the invention, a polypeptide of the invention is immunogenic. That is, the polypeptide can elicit an immune response when it is administered to an animal.

In one embodiment of the invention, a polypeptide or fragment thereof is isolated. Isolated means that a polypeptide of the invention is substantially free from other biological molecules. A substantially isolated polypeptide is at least about 75%, 80%, 90%, 95%, 97%, 99% or 100% pure by dry weight. Purity can be measured by a method such as column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis.

The invention also includes functionally active variants of polypeptides shown in SEQ ID NOs:167-226, 228-261, and 263-354. In one embodiment, the polypeptide includes an amino acid sequence at least about 75% identical to a sequence shown as SEQ ID NOs:167-226, 228-261, and 263-354, or a fragment thereof. The polypeptide can be at least about 75%, 80%, 85%, 90%, 95%, 98%, 99% or more identical to SEQ ID NOs:167-226, 228-261, and 263-354, and specifically binds to a Pg-specific antibody, antibody fragment, single-chain antibody or aptamer of the invention.

Specifically binds means that the polypeptide recognizes and binds to an antibody of the invention with greater affinity than to other, non-specific molecules. For example, an antibody raised against an antigen (e.g., a polypeptide) to which it binds more efficiently than to a non-specific protein can be described as specifically binding to the antigen. Binding specifically can be tested using, for example, an enzyme-linked immunosorbant assay (ELISA), a radioimmunoassay (RIA), or a western blot assay using methodology well known in the art.

A polypeptide is a functionally active variant if it reacts substantially the same as a polypeptide shown in SEQ ID NOs:167-226, 228-261, and 263-354 or an immunogenic fragment thereof in an assay such as an immunohistochemical assay, an ELISA, an RIA, or a western blot assay, e.g. has 90-110% of the specific binding activity of the original polypeptide. In one embodiment, the assay is a competition assay wherein the functionally active variant polypeptide is capable of reducing binding of a polypeptide shown in SEQ ID NOs:167-226, 228-261, and 263-354 to a corresponding antibody, antibody fragment, single-chain antibody or aptamer by about 80, 95, 99, or 100%.

Functionally active variants can also comprise “polypeptide fragments” of the invention. Polypeptide fragments comprise or consist essentially of about at least 5, 10, 25, 50, 75, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 1,500, or 2,000 amino acids of SEQ ID NOs:167-226, 228-261, and 263-354.

As used herein, percent identity of two amino acid sequences (or of two nucleic acid sequences) is determined using the algorithm of Karlin and Altschul (PNAS USA 87:2264-2268, 1990), modified as in Karlin and Altschul, PNAS USA 90:5873-5877, 1993). Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. (J. Mol. Biol. 215:403-410, 1990). BLAST nucleotide searches are performed with the NBLAST program, score=100, wordlength=12. BLAST protein searches are performed with the XBLAST program, score=50, wordlength=3. To obtain gapped alignment for comparison purposes GappedBLAST is utilized as described in Altschul et al. (Nucleic Acids Res. 25:3389-3402, 1997). When utilizing BLAST and GappedBLAST programs the default parameters of the respective programs (e.g., XBLAST and NBLAST) are used to obtain nucleotide sequences homologous to a nucleic acid molecule of the invention.

Identity or identical means amino acid sequence similarity and has an art recognized meaning. Sequences with identity share identical or similar amino acids. Thus, a candidate sequence sharing 85% amino acid sequence identity with a reference sequence requires that, following alignment of the candidate sequence with the reference sequence, 85% of the amino acids in the candidate sequence are identical to the corresponding amino acids in the reference sequence, and/or constitute conservative amino acid changes.

Functionally active variants of SEQ ID NOs:167-226, 228-261, and 263-354 retain substantially the same functional activity of the original polypeptide or fragment. Naturally occurring functionally active variants such as allelic variants and species variants and non-naturally occurring functionally active variants are included in the invention and can be produced by, for example, mutagenesis techniques or by direct synthesis.

A functionally active variant differs by about, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20 50, or 100 amino acid residues from a polypeptide shown in SEQ ID NOs:167-226, 228-261, and 263-354 or a fragment thereof. Where this comparison requires alignment the sequences are aligned for maximum homology. The site of variation can occur anywhere in the polypeptide, as long as activity substantially similar to a polypeptide shown in SEQ ID NOs:167-226, 228-261, and 263-354 are maintained within the functionally active variant.

Guidance concerning how to make phenotypically silent amino acid substitutions is provided in Bowie et al., Science, 247:1306-1310 (1990), which teaches that there are two main strategies for studying the tolerance of an amino acid sequence to change.

The first strategy exploits the tolerance of amino acid substitutions by natural selection during the process of evolution. By comparing amino acid sequences in different species, the amino acid positions which have been conserved between species can be identified. These conserved amino acids are likely important for protein function. In contrast, the amino acid positions in which substitutions have been tolerated by natural selection indicate positions which are not critical for protein function. Thus, positions tolerating amino acid substitution can be modified while still maintaining specific binding activity of the polypeptide.

The second strategy uses genetic engineering to introduce amino acid changes at specific positions of a cloned gene to identify regions critical for protein function. For example, site-directed mutagenesis or alanine-scanning mutagenesis (the introduction of single alanine mutations at every residue in the molecule) can be used (Cunningham et al., Science, 244:1081-1085 (1989)). The resulting variant molecules can then be tested for specific binding to antibodies of the invention.

According to Bowie et al., these two strategies have revealed that proteins are surprisingly tolerant of amino acid substitutions. The authors further indicate which amino acid changes are likely to be permissive at certain amino acid positions in the protein. For example, the most buried or interior (within the tertiary structure of the protein) amino acid residues require nonpolar side chains, whereas few features of surface or exterior side chains are generally conserved.

Methods of introducing a mutation into amino acids of a protein is well known to those skilled in the art. See, e.g., Ausubel (ed.), Current Protocols in Molecular Biology, John Wiley and Sons, Inc. (1994); T. Maniatis, E. F. Fritsch and J. Sambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor laboratory, Cold Spring Harbor, N.Y. (1989)). Mutations can also be introduced using commercially available kits such as “QuikChange™ Site-Directed Mutagenesis Kit” (Stratagene). The generation of a functionally active variant of a polypeptide by replacing an amino acid that does not influence the function of a polypeptide can be accomplished by one skilled in the art.

A polypeptide of the invention can be isolated from cell sources using standard protein purification techniques. Polypeptides of the invention can also be synthesized chemically or produced by recombinant DNA techniques. For example, a polypeptide of the invention can be synthesized using conventional peptide synthesizers. Additionally, a polynucleotide encoding a polypeptide of the invention can be introduced into an expression vector that can be expressed in a suitable expression system using techniques well known in the art. A variety of bacterial, yeast, plant, mammalian, and insect expression systems are available in the art and any such expression system can be used. Optionally, a polynucleotide encoding a polypeptide of the invention can be translated in a cell-free translation system.

A functionally active variant polypeptide can be also isolated using a hybridization technique. Briefly, DNA having a high homology to the whole or part of a nucleic acid sequence encoding SEQ ID NOs:167-226, 228-261, and 263-354 is used to prepare a functionally active polypeptide. Therefore, a polypeptide of the invention also includes polypeptides that are functionally equivalent to a SEQ ID NOs:167-226, 228-261, and 263-354 and are encoded by a nucleic acid molecule that hybridizes with a nucleic acid encoding SEQ ID NOs:167-226, 228-261, and 263-354 or a complement thereof. One of skill in the art can easily determine nucleic acid sequences that encode polypeptides of the invention using readily available codon tables. As such, these nucleic acid sequences are not presented herein.

The stringency of hybridization for a nucleic acid encoding a polypeptide that is a functionally active variant is, for example, 10% formamide, 5×SSPE, 1× Denhart's solution, and 1× salmon sperm DNA (low stringency conditions). More preferable conditions are, 25% formamide, 5×SSPE, 1× Denhart's solution, and 1× salmon sperm DNA (moderate stringency conditions), and even more preferable conditions are, 50% formamide, 5×SSPE, 1× Denhart's solution, and 1× salmon sperm DNA (high stringency conditions). However, several factors influence the stringency of hybridization other than the above-described formamide concentration, and one skilled in the art can suitably select these factors to accomplish a similar stringency.

Nucleic acid molecules encoding a functionally active variant polypeptide can also be isolated by a gene amplification method such as PCR using a portion of a nucleic acid molecule DNA encoding a polypeptide shown in SEQ ID NOs:167-226, 228-261, and 263-354 as the probe.

Functionally active variant polypeptides of the invention can also comprise those that arise as a result of the existence of multiple genes, alternative transcription events, alternative RNA splicing events, and alternative translational and postranslational events. A polypeptide can be expressed in systems, e.g., cultured cells, which result in substantially the same postranslational modifications present as when the polypeptide is expressed in a native cell, or in systems that result in the alteration or omission of postranslational modifications, e.g., glycosylation or cleavage, present when expressed in a native cell.

A polypeptide of the invention can be produced as a fusion protein that contains other non-Pg or non-Pg-derived amino acid sequences (i.e., heterologous polypeptides), such as amino acid linkers or signal sequences, as well as ligands useful in protein purification, such as glutathione-S-transferase, histidine tag, and staphylococcal protein A. More than one polypeptide of the invention can be present in a fusion protein. The heterologous polypeptide can be fused, for example, to the N-terminus or C-terminus of the polypeptide. A polypeptide of the invention can also comprise homologous amino acid sequences, i.e., other Pg or Pg-derived sequences.

In one embodiment of the invention, functionally active variants differ from polypeptides shown in SEQ ID NOs:167-226, 228-261, and 263-354 by only conservative amino acid substitutions, such that the antigenic properties of the polypeptide are substantially the same as the original polypeptide. These variants can generally be identified by modifying one of the polypeptide sequences of the invention, and evaluating the antigenic properties of the modified polypeptide using, for example, an immunohistochemical assay, an enzyme-linked immunosorbant assay (ELISA), a radioimmunoassay (RIA), or a western blot assay. These variants can comprise at least about 1, 5, 10, 25, 50, or 100 conservative amino acid substitutions.

A conservative amino acid substitution is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged. In general, the following groups of amino acids represent conservative changes: (1) ala, pro, gly, glu, asp, gln, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his.

More particularly, a “conservative amino acid substitution” may involve a substitution of a native amino acid residue with a normative residue such that there is little or no effect on the polarity or charge of the amino acid residue at that position. Furthermore, any native residue in the polypeptide may also be substituted with alanine, as has been previously described for “alanine scanning mutagenesis.”

Conservative amino acid substitutions also encompass non-naturally occurring amino acid residues that are typically incorporated by chemical peptide synthesis rather than by synthesis in biological systems. These include peptidomimetics, and other reversed or inverted forms of amino acid moieties.

Naturally occurring residues may be divided into classes based on common side chain properties:

1) hydrophobic: norleucine, Met, Ala, Val, Leu, Ile;

2) neutral hydrophilic: Cys, Ser, Thr;

3) acidic: Asp, Glu;

4) basic: Asn, Gln, His, Lys, Arg;

5) residues that influence chain orientation: Gly, Pro; and

6) aromatic: Trp, Tyr, Phe.

For example, non-conservative substitutions may involve the exchange of a member of one of these classes for a member from another class.

In making such changes, the hydropathic index of amino acids may be considered. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics. The hydropathic indices are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5); lysine (−3.9); and arginine (−4.5).

The importance of the hydropathic amino acid index in conferring interactive biological function on a protein is generally understood in the art (Kyte et al., 1982, J. Mol. Biol. 157:105-31). It is known that certain amino acids may be substituted for other amino acids having a similar hydropathic index or score and still retain a similar biological activity. In making changes based upon the hydropathic index, the substitution of amino acids whose hydropathic indices are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.

It is also understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity, particularly where the biologically functionally equivalent protein or peptide thereby created is intended for use in immunological embodiments, as in the present case. The greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with its immunogenicity and antigenicity, i.e., with a biological property of the protein.

The following hydrophilicity values have been assigned to these amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine (−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5); and tryptophan (−3.4). In making changes based upon similar hydrophilicity values, the substitution of amino acids whose hydrophilicity values are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred. One may also identify epitopes from primary amino acid sequences on the basis of hydrophilicity. These regions are also referred to as “epitopic core regions.”

Desired amino acid substitutions (whether conservative or non-conservative) can be determined by those skilled in the art at the time such substitutions are desired. Exemplary amino acid substitutions are set forth in Table 1.

TABLE 1 Original Exemplary Preferred Residues Substitutions Substitutions Ala Val, Leu, Ile Val Arg Lys, Gln, Asn Lys Asn Gln Gln Asp Glu Glu Cys Ser, Ala Ser Gln Asn Asn Glu Asp Asp Gly Pro, Ala Ala His Asn, Gln, Lys, Arg Arg Ile Leu, Val, Met, Ala, Leu Phe, Norleucine Leu Norleucine, Ile, Ile Val, Met, Ala, Phe Lys Arg, 1,4 Diamino-butyric Arg Acid, Gln, Asn Met Leu, Phe, Ile Leu Phe Leu, Val, Ile, Ala,, Tyr Leu Pro Ala Gly Ser Thr, Ala, Cys Thr Thr Ser Ser Trp Tyr, Phe Tyr Tyr Trp, Phe, Thr, Ser Phe Val Ile, Met, Leu, Phe, Leu Ala, Norleucine

Polypeptides of the invention can be antigens that are recognized by an antibody reactive against Pg. The antigen can comprise one or more epitopes (or antigenic determinants). An epitope can be a linear epitope, sequential epitope or a conformational epitope. Epitopes within a polypeptide of the invention can be identified by several methods. See, e.g., U.S. Pat. No. 4,554,101; Jameson & Wolf, CABIOS 4:181-186 (1988). For example, a polypeptide of the invention can be isolated and screened. A series of short peptides, which together span an entire polypeptide sequence, can be prepared by proteolytic cleavage. By starting with, for example, 100-mer polypeptide fragments, each fragment can be tested for the presence of epitopes recognized in an ELISA. For example, in an ELISA assay a Pg polypeptide, such as a 100-mer polypeptide fragment, is attached to a solid support, such as the wells of a plastic multi-well plate. A population of antibodies are labeled, added to the solid support and allowed to bind to the unlabeled antigen, under conditions where non-specific adsorbtion is blocked, and any unbound antibody and other proteins are washed away. Antibody binding is detected by, for example, a reaction that converts a colorless substrate into a colored reaction product. Progressively smaller and overlapping fragments can then be tested from an identified 100-mer to map the epitope of interest.

Polynucleotides

Polynucleotides of the invention contain less than an entire genome and can be RNA or single- or double-stranded DNA or combinations or modifications thereof. The polynucleotides can be isolated free of other components, such as proteins and lipids. An isolated polynucleotide is substantially purified away from other polynucleotides and biological molecules. Preferably, a polynucleotide is greater than 60%, 70%, 80%, 90%, 95%, 98%, 99%, 99.5% or more purified from other polynucleotides and/or biological molecules. The polynucleotides of the invention encode the polypeptides described above, as well as fragments thereof. Polynucleotides of the invention also include those shown in SEQ ID NO:1-166, 227, and 262 and fragments thereof. These polynucleotides will be referred to as the “polynucleotide SEQ IDs.”

One of skill in the art can obtain a polynucleotide sequence of the invention using a disclosed polypeptide sequence of the invention and codon tables. Polynucleotides can contain naturally occurring polynucleotides or sequences that differ from those of any naturally occurring sequences or polynucleotides. Polynucleotides of the invention can differ from naturally occurring nucleic acids, but still encode naturally occurring amino acids due to the degeneracy of the genetic code. These polynucleotides are degenerate variants and one of skill in the art could determine the sequences of all degenerate variant polynucleotides that encode SEQ ID NOs:167-226, 228-261, and 263-354. As such, these sequences are not presented herein. Polynucleotides of the invention can also comprise other heterologous nucleotide sequences (i.e., heterologous polynucleotides), such as sequences coding for linkers, signal sequences, heterologous signal sequences, TMR stop transfer sequences, transmembrane domains, or ligands useful in protein purification such as glutathione-S-transferase, histidine tag, and staphylococcal protein A. Polynucleotides of the invention can also comprise other homologous nucleotide sequences, i.e., other Pg or Pg-derived sequences.

An isolated polynucleotide is a nucleic acid molecule that is not immediately contiguous with 5′ and 3′ flanking sequences with which it is normally contiguous when present in a naturally occurring genome. Therefore, an isolated polynucleotide can be, for example, a polynucleotide that is incorporated into a vector, such as a plasmid or viral vector, a polynucleotide that is incorporated into the genome of a heterologous cell (or the genome of a homologous cell, but at a site different from that where it naturally occurs) and a polynucleotide that exists as a separate molecule such as a polynucleotide produced by PCR amplification, chemical synthesis, restriction enzyme digestion, or in vitro transcription. An isolated polynucleotide is also a nucleic acid molecule, such as a recombinant nucleic acid molecule that forms part of hybrid polynucleotide encoding additional polypeptide sequences that can be used for example, in the production of a fusion protein.

Degenerate nucleotide sequences encoding polypeptides of the invention, as well as homologous variant nucleotide sequences that are at least about 75, or about 90, 96, 98, or 99% identical to the nucleotide sequences shown in the polynucleotide SEQ IDs and the complements thereof are also included in the invention. Percent sequence identity can be calculated as described in the “Polypeptides” section. Degenerate nucleotide sequences are polynucleotides that encode a polypeptide shown in the polypeptide SEQ IDs or fragments thereof, but differ in nucleic acid sequence from the sequence given in the polynucleotide SEQ IDs or nucleic acid sequences occurring in nature, due to the degeneracy of the genetic code. Complementary DNA (cDNA) molecules of Pg polynucleotides that encode biologically functional Pg polypeptides also are Pg polynucleotides. A polynucleotide of the invention can comprise about at least 5, 10, 15, 50, 100, 200, 250, 300, 400, 500, or 600 contiguous nucleotides of a nucleic acid sequence shown in the polynucleotide SEQ IDs.

Polynucleotides of the invention can be isolated from nucleic acid sequences present in, for example, a biological sample, such as plaque, saliva, crevicular fluid, sputum, blood, serum, plasma, urine, feces, cerebrospinal fluid, amniotic fluid, wound exudate, or tissue, from an infected individual. Polynucleotides can also be synthesized in the laboratory, for example, using an automatic synthesizer. An amplification method such as PCR can be used to amplify polynucleotides from either genomic DNA or cDNA encoding the polypeptides.

A polynucleotide can also comprise one or more expression control sequences such as promoters, origins of replication, or enhancers, for example. A polynucleotide of the invention can be present in a vector, such as, for example, an expression vector. If desired, polynucleotides can be cloned into an expression vector comprising, for example, origins of replication, promoters, enhancers, or other expression control sequences that drive expression of the polynucleotides of the invention in host cells. The polynucleotides can be operably linked to the expression control sequences. That is, linked such that the expression control sequences drive expression of the polynucleotides. An expression vector can be, for example, a plasmid, such as pBR322, pUC, or ColE1, or an adenovirus vector, such as an adenovirus Type 2 vector or Type 5 vector. Optionally, other vectors can be used, including but not limited to Sindbis virus, simian virus 40, alphavirus vectors, poxvirus vectors, and cytomegalovirus and retroviral vectors, such as murine sarcoma virus, mouse mammary tumor virus, Moloney murine leukemia virus, and Rous sarcoma virus. Vectors suitable for use in the present invention include, for example, bacterial vectors, mammalian vectors, viral vectors (such as retroviral, adenoviral, adeno-associated viral, herpes virus, simian virus 40 (SV40), and bovine papilloma virus vectors) and baculovirus-derived vectors for use in insect cells. Minichromosomes such as MC and MC 1, bacteriophages, phagemids, yeast artificial chromosomes, bacterial artificial chromosomes, virus particles, virus-like particles, cosmids (plasmids into which phage lambda cos sites have been inserted) and replicons (genetic elements that are capable of replication under their own control in a cell) can also be used. Polynucleotides in such vectors can be operably linked to a promoter, which is selected based on, e.g., the cell type in which expression is sought. Methods for preparing polynucleotides operably linked to an expression control sequence and expressing them in a host cell are well-known in the art. See, e.g., U.S. Pat. No. 4,366,246.

Host cells into which vectors, such as expression vectors, comprising polynucleotides of the invention can be introduced include, for example, prokaryotic cells (e.g., bacterial cells) and eukaryotic cells (e.g., yeast cells; insect cells; and mammalian cells). Such host cells are available from a number of different sources that are known to those skilled in the art, e.g., the American Type Culture Collection (ATCC), Rockville, Md. Host cells into which the polynucleotides of the invention have been introduced, as well as their progeny, even if not identical to the parental cells, due to mutations, are included in the invention.

Methods for introducing polynucleotides of the invention (e.g., vectors comprising the polynucleotides or naked polynucleotides) into cells (e.g., bacterial, yeast, insect or mammalian cells), either transiently or stably, are well known in the art. For example, transformation methods using standard CaCl₂, MgCl₂, or RbCl methods, protoplast fusion methods or transfection of naked or encapsulated nucleic acids using calcium phosphate precipitation, cellular fusion, microinjection, viral infection, and electroporation.

Isolation and purification of polypeptides produced in the systems described above can be carried out using conventional methods, appropriate for the particular system. For example, preparative chromatography and immunological separations employing antibodies, such as monoclonal or polyclonal antibodies, can be used.

Polynucleotides can be synthesized in the laboratory, for example, using an automatic synthesizer. An amplification method such as PCR can be used to amplify polynucleotides from either genomic DNA or cDNA encoding the polypeptides.

Antibodies

Antibodies, such as monoclonal and polyclonal antibodies, antibody fragments, and single-chain antibodies that specifically bind to polypeptides of the invention are part of the invention. An antibody and antigen (e.g., a polypeptide or polypeptide fragment of the invention) specifically bind to each other if they bind to each other with greater affinity than to other, non-specific molecules. For example, an antibody raised against an antigen to which it binds more efficiently than to a non-specific protein can be described as specifically binding to the antigen.

An antibody is said to be “directed against” a molecule if it is capable of specifically reacting with the molecule and specifically binding the molecule. An epitope refers to that portion of any molecule capable of being bound by an antibody which can also be recognized by that antibody. Epitopes or “antigenic determinants” usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and have specific three-dimensional structural characteristics as well as specific charge characteristics.

Polypeptides of the invention comprise at least one epitope. An epitope is an antigenic determinant of a polypeptide. Epitopes within a polypeptide of the invention can be identified by several methods. See, e.g., U.S. Pat. No. 4,554,101; Jameson & Wolf, CABIOS 4:181-186 (1988) and “Polypeptide” section above.

An antibody is an intact immunoglobulin molecule, a fragment of an immunoglobulin molecule, or a single-chain antibody that specifically binds to a polypeptide of the invention (e.g., SEQ ID NOs:167-226, 228-261, and 263-354 and/or fragments thereof). An antibody of the invention can be any antibody class, including for example, IgG, IgM, IgA, IgD and IgE.

Antibodies of the invention can be chimeric (see, e.g., U.S. Pat. No. 5,482,856), humanized (see, e.g., Jones et al., Nature 321:522 (1986); Reichmann et al., Nature 332:323 (1988); Presta, Curr. Op. Struct. Biol. 2:593 (1992)), or human antibodies. Human antibodies can be made by, for example, direct immortilization, phage display, transgenic mice, or a Trimera methodology, see e.g., Reisener et al., Trends Biotechnol. 16:242-246 (1998).

Antibody fragments of the invention retain some ability to selectively bind to the antigen (e.g., a polypeptide of the invention) from which they are derived, and can be made using well known methods in the art. In one embodiment of the invention, an antibody, antibody fragment or single-chain antibody comprises all such antibodies that specifically bind to a polypeptide of the invention (e.g., SEQ ID NOs:167-226, 228-261, and 263-354 and/or fragments thereof). Fragments of antibodies are a portion of an intact antibody comprising the antigen binding site or variable region of an intact antibody, wherein the portion is free of the constant heavy chain domains of the Fc region of the intact antibody. Examples of antibody fragments include Fab, Fab′, Fab′-SH and F(ab′)₂ fragments.

Antigens that can be used in producing antibodies of the invention include polypeptides and polypeptide fragments of the invention. Antibodies of the invention can be made, for example, by using a polypeptide or a polypeptide fragment that contains an epitope present in a polypeptide shown in SEQ ID NOs:167-226, 228-261, and 263-354 as an immunogen in standard antibody production methods (see e.g., Kohler et al., Nature, 256:495, 1975; Ausubel et al. (1992) Current Protocols in Molecular Biology, John Wylie and Sons, Inc. New York, N.Y.; Harlow and Lane, Eds, (1988) Current Edition, Antibodies: A Laboratory Manual, Cold Spring Harbor Press, N.Y). A polypeptide used to immunize an animal can be obtained by standard recombinant, chemical synthetic, or purification methods. As is well known in the art, in order to increase immunogenicity, an antigen can be conjugated to a carrier protein. Commonly used carriers include keyhole limpet hemocyanin (KLH), thyroglobulin, bovine serum albumin (BSA), and tetanus toxoid. The coupled peptide is then used to immunize an animal (e.g., a mouse, a rat, or a rabbit). In addition to such carriers, well known adjuvants can be administered with the antigen to facilitate induction of a strong immune response.

An antibody can be made in vivo in suitable laboratory animals or in vitro using recombinant DNA techniques. Means for preparing and characterizing antibodies are well know in the art. See, e.g., Dean, Methods Mol. Biol. 80:23-37 (1998); Dean, Methods Mol. Biol. 32:361-79 (1994); Baileg, Methods Mol. Biol. 32:381-88 (1994); Gullick, Methods Mol. Biol. 32:389-99 (1994); Drenckhahn et al. Methods Cell. Biol. 37:7-56 (1993); Morrison, Ann. Rev. Immunol. 10:239-65 (1992); Wright et al. Crit. Rev. Immunol. 12:125-68 (1992). For example, polyclonal antibodies can be produced by administering a polypeptide of the invention to an animal, such as a human or other primate, mouse, rat, rabbit, guinea pig, goat, pig, cow, sheep, donkey, or horse. Serum from the immunized animal is collected and the antibodies are purified from the plasma by, for example, precipitation with ammonium sulfate, followed by chromatography, such as affinity chromatography. Techniques for producing and processing polyclonal antibodies are known in the art.

Monoclonal antibodies directed against epitopes present on a polypeptide of the invention can also be readily produced. For example, normal B cells from a mammal, such as a mouse, which was immunized with a polypeptide of the invention can be fused with, for example, HAT-sensitive mouse myeloma cells to produce hybridomas. Hybridomas producing Pg-specific antibodies can be identified using RIA or ELISA and isolated by cloning in semi-solid agar or by limiting dilution. Clones producing Pg-specific antibodies are isolated by another round of screening. Monoclonal antibodies can be screened for specificity using standard techniques, for example, by binding a polypeptide of the invention to a microtiter plate and measuring binding of the monoclonal antibody by an ELISA assay. Techniques for producing and processing monoclonal antibodies are known in the art. See e.g., Kohler & Milstein, Nature, 256:495 (1975). Particular isotypes of a monoclonal antibody can be prepared directly, by selecting from the initial fusion, or prepared secondarily, from a parental hybridoma secreting a monoclonal antibody of a different isotype by using a sib selection technique to isolate class-switch variants. See Steplewski et al., P.N.A.S. U.S.A. 82:8653 1985; Spria et al., J. Immunolog. Meth. 74:307, 1984. Monoclonal antibodies of the invention can also be recombinant monoclonal antibodies. See, e.g., U.S. Pat. No. 4,474,893; U.S. Pat. No. 4,816,567. Antibodies of the invention can also be chemically constructed. See, e.g., U.S. Pat. No. 4,676,980.

Polyclonal and monoclonal antibodies can be purified, for example, by binding to, and elution from, a matrix containing a polypeptide or polypeptide fragment of the invention to which the antibodies were raised. Additional methods for antibody purification and concentration are well known in the art and can be practiced with the antibodies of the invention. Anti-idiotype antibodies corresponding to polypeptides of the invention are also included in the invention, and can be produced using standard methods.

Antibodies, antibody fragments, and single-chain antibodies of the invention can further be used to isolate Pg organisms or Pg antigens by immunoaffinity columns. The antibodies can be affixed to a solid support by, for example, adsorbtion or by covalent linkage so that the antibodies retain their immunoselective activity. Optionally, spacer groups can be included so that the antigen binding site of the antibody remains accessible. The immobilized antibodies can then be used to bind Pg organisms or Pg antigens from a sample, such as a biological sample including saliva, plaque, crevicular fluid, sputum, blood, urine, feces, cerebrospinal fluid, amniotic fluid, wound exudate, or tissue. The bound Pg organisms or Pg antigens are recovered from the column matrix by, for example, a change in pH.

Antibodies of the invention can also be used in immunolocalization studies to analyze the presence and distribution of a polypeptide of the invention during various cellular events or physiological conditions. Antibodies can also be used to identify molecules involved in passive immunization and to identify molecules involved in the biosynthesis of non-protein antigens. Identification of such molecules can be useful in vaccine development. Antibodies of the invention, including, for example, monoclonal antibodies and single-chain antibodies, can be used to monitor the course of amelioration of a disease caused by Pg. By measuring the increase or decrease of Pg antibodies to Pg proteins in a test sample from an animal, it can be determined whether a particular therapeutic regimen aimed at ameliorating the disorder is effective. Antibodies can be detected and/or quantified using for example, direct binding assays such as RIA, ELISA, or western blot assays.

Aptamers of the Invention

An aptamer is a nucleic acid molecule (e.g., DNA or RNA or analogs thereof) that is capable of binding to a particular target molecule (e.g., a protein or polypeptide) with high affinity and specificity. See e.g., Tuerk and Gold, Science 249:505 (1990), Ellington and Szostak, Nature, 346:818 (1990).

Aptamers can bind protein targets and disrupt the interactions of the protein target with other proteins and/or disrupt catalysis by the protein targets. See e.g., Blind et al., Proc. Natl. Acad. Sci., 96:3606-3610 (1999); U.S. Pat. No. 5,756,291; U.S. Pat. No. 5,840,867; Osborne et al., Curr. Opin. Chem. Biol. 1:5-9 (1997).

Aptamers of the invention have specific binding regions that form complexes with a polypeptide shown in SEQ ID NOs:167-226, 228-261, and 263-354 and/or fragments thereof under conditions where other non-specific substances are not complexed with the aptamer. Aptamers of the invention can also complex with a protein comprising SEQ ID NOs:167-226, 228-261, and 263-354 and/or fragments thereof under conditions where other non-specific substances are not complexed with the aptamer. The specificity of binding is defined in terms of comparative dissociation constants (Kd) of an aptamer for its ligand (in this case SEQ ID NOs:167-226, 228-261, and 263-354 and/or fragments thereof) as compared to the dissociation constant of the aptamer for other non-specific substances. Typically, the Kd of an aptamer for its ligand is about 10-fold less that the Kd for the aptamer for non-specific substances. In other embodiments, the Kd is about 50-fold, 100-fold, or 200-fold less that the Kd for the aptamer for non-specific substances. An aptamer can be, for example, 10, 20, 50, 100, 150, 200, 300, 400, or 500 nucleotides in length.

Aptamers can be identified for a specific polypeptide or protein target using for, example, selective evolution of ligands by exponential enrichment (SELEX) methods. See e.g., Wilson and Szoztak, Ann. Rev. Biochem. 68:611-647 (1999); Sun, Curr. Opin. Mol. Ther. 2:100-5 (2000); U.S. Pat. No. 5,861,254; U.S. Pat. No. 5,475,096; U.S. Pat. No. 5,595,877; U.S. Pat. No. 5,660,985; see also, U.S. Pat. No. 6,180,348; Bock et al., Nature, 355:564-566 (1990); Conrad et al., Methods in Enzymol., 267:336-367 (1996).

Methods of Diagnosis or Pg Infection and Detection of Pg

Antibodies, antibody fragments, single-chain antibodies, polypeptides and polynucleotides of the invention can be used to detect Pg organisms, Pg polynucleotides, Pg polypeptides, and Pg-specific antibodies in a test sample, such as a biological sample.

A biological sample can be, for example, plaque, saliva, crevicular fluid, sputum, blood, serum, plasma, urine, feces, cerebrospinal fluid, amniotic fluid, wound exudates or tissue.

An antibody, antibody fragment, or single-chain antibody of the invention can be used to detect Pg infection, the presence of Pg polypeptides or fragments thereof, and/or Pg organisms by contacting a test sample suspected of containing a Pg polypeptide, fragment thereof, or Pg organisms (i.e., antigens) with an antibody of the invention under conditions enabling the formation of an antibody-antigen complex (i.e., an immunocomplex). The amount of antibody-antigen complexes can be determined by methodology known in the art. A level that is higher than that formed in a control sample indicates a Pg infection and/or the presence of a Pg polypeptide, fragment thereof, and/or Pg organism in the test sample.

Methods of detection of an antigen in test sample using an antibody, antibody fragment, or single-chain antibody are well known in the art and any such method can be used. Antibodies of the invention can be used in vitro or in vivo for immunodiagnosis. The antibodies are suited for use in, for example, immunoassays in which they are in liquid phase or bound to a solid phase carrier. Antibodies, fragments thereof, and/or single-chain antibodies of the invention can be bound to a support and used to detect the presence of Pg or a Pg antigen. Supports include, for example, glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, agaroses and magletite.

The antibodies used in such immunoassays can be detectably labeled (e.g., with an enzyme, a radioisotope, a fluorescent compound, a colloidal metal, a chemiluminescent compound, a phosphorescent compound, or a bioluminescent compound) using any of several standard methods that are well known in the art. Alternatively, the antibodies can be unlabeled. Examples of immunoassays in which the antibodies of the invention can be used include, e.g., competitive and non-competitive immunoassays, which are carried out using either direct or indirect formats. Examples of such immunoassays include radioimmunoassays (RIA) and sandwich assays (e.g., enzyme-linked immunosorbent assays (ELISAs)). Detection of Pg polypeptides using antibodies of the invention can be done using immunoassays that are run in either forward, reverse, or simultaneous modes, including immunohistochemical assays on physiological samples. Other immunoassay formats are well known in the art, and can be used in the invention.

An immunoassay can utilize one antibody or several antibodies. An immunoassay can use, for example, a monoclonal antibody directed towards a Pg epitope, a combination of monoclonal antibodies directed towards epitopes of one Pg polypeptide, monoclonal antibodies directed towards epitopes of different Pg polypeptides, polyclonal antibodies directed towards the same Pg antigen, polyclonal antibodies directed towards different Pg antigens, or a combination of monoclonal and polyclonal antibodies.

An antibody of the invention can be used in a method of the diagnosis of Pg infection by obtaining a test sample from an animal suspected of having a Pg infection. The test sample is contacted with an antibody of the invention under conditions enabling the formation of an antibody-antigen complex (i.e., an immunocomplex). The presence and/or amount of antibody-antigen complexes can be determined by methodology known in the art. The presence of complexes and/or a level of complexes that is higher than that formed in a control sample indicates a Pg infection.

One embodiment of the invention provides methods of detecting the presence of Pg or a Pg polypeptide in a test sample. The methods comprise contacting a test sample with an antibody, antibody fragment, or single-chain antibody of the invention that specifically binds Pg or a Pg polypeptide under conditions that allow formation of an immunocomplex between the antibody, antibody fragment, or single-chain antibody and the Pg or the Pg polypeptide. Detection of an immunocomplex indicates the presence of Pg or a Pg polypeptide in the test sample. The detected Pg polypeptide can be expressed in vivo during infection of an animal.

Another embodiment of the invention provides methods for detecting Pg infection in a subject. The methods comprise obtaining a biological sample from a subject and contacting the biological sample with an immunogenic polypeptide comprising at least about 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354 under conditions that allow formation of the immunocomplexes between the polypeptide and Pg antibodies present in the biological sample. Immunocomplexes are detected. The detection of immunocomplexes indicates a Pg infection in the subject. Alternatively or additionally the amount of immunocomplexes can be detected and the amount of immunocomplexes formed is compared to a control sample. A higher amount of immunocomplexes in the biological sample than the control sample indicates a Pg infection in the subject. Additionally, the isotype or isotypes of antibodies present in immunocomplexes or the ratios of isotypes present in immunocomplexes as compared to controls can be used to indicate Pg infection.

Another embodiment of the invention provides methods for detecting Pg in a subject. The methods comprise obtaining a biological sample from the subject and contacting the biological sample with an antibody, antibody fragment, or single-chain antibody of the invention under conditions that allow formation of immunocomplexes between the antibody, antibody fragment, or single-chain antibody and Pg polypeptides present in the biological sample. Immunocomplexes are detected. The detection of immunocomplexes indicates a Pg infection in the subject. Alternatively or additionally the amount of immunocomplexes is detected. The amount of immunocomplexes formed is compared to a control sample. A higher amount of immunocomplexes in the biological sample than in the control sample indicates a Pg infection in the subject.

In another embodiment of the invention, a polypeptide or fragment thereof of the invention can be used in a method of detecting Pg infection or the presence of antibodies or antibody fragments specific for Pg by contacting a test sample suspected of containing a Pg antibody or antibody fragment with a polypeptide or fragment thereof (i.e., an antigen) of the invention under conditions enabling the formation of an antibody-antigen complex (i.e., an immunocomplex). The polypeptide or fragment can be labeled or unlabeled. The presence of antibody-antigen complexes can be determined by methodology known in the art. Detection of the immunocomplex indicates the presence of a Pg antibody or Pg antibody fragment in a test sample. A control reaction can also be completed, wherein a level of immunocomplexes in a test sample that is higher than that formed in a control sample indicates a Pg infection or the presence of antibodies specific for Pg in the test sample. The same methodologies and techniques described above for the detection of polypeptides can be used to detect Pg antibodies.

Polynucleotides and fragments thereof the invention can be used, for example, as probes or primers, for example PCR primers, to detect the presence of Pg polynucleotides in a test sample, such as a biological sample. The ability of such probes and primers to specifically hybridize to Pg polynucleotide sequences will enable them to be of use in detecting the presence of complementary sequences in a given sample. Polynucleotides from the sample can be, for example, subjected to gel electrophoresis or other size separation techniques or can be immobilized without size separation. The polynucleotide probes or primers can be labeled or unlabeled. Suitable labels, and methods for labeling probes and primers are known in the art, and include, for example, radioactive labels incorporated by nick translation or by kinase, biotin labels, fluorescent labels, chemiluminescent labels, bioluminescent labels, metal chelator labels and enzyme labels. The polynucleotides from the sample are contacted with the probes or primers under hybridization conditions of suitable stringencies.

One embodiment of the invention provides methods of detecting the presence of a first Pg polynucleotide in a test sample. The methods comprise contacting a test sample suspected of containing the first polynucleotide with a second polynucleotide under hybridization conditions. The second polynucleotide is an isolated polynucleotide comprising a sequence that encodes an isolated immunogenic polypeptide comprising about at least 5 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs:167-226, 228-261, and 263-354. A hybridized first and second polynucleotide complex is detected. The presence of a hybridized first and second polynucleotide complex indicates the presence of a first polynucleotide in the test sample.

One embodiment of the invention provides methods for detecting Pg in a subject. The methods comprise obtaining a biological sample from the subject and contacting the biological sample with the polynucleotide of the invention under conditions that allow the formation of a hybridized complex between the polynucleotide of the invention and Pg polynucleotides present in the biological sample. The amount of hybridized complexes are detected and optionally compared to a control sample. The presence of hybridized complexes or a higher amount of hybridized complexes in the biological sample than in the control sample indicates a Pg infection in the subject.

Depending on the application, varying conditions of hybridization can be used to achieve varying degrees of selectivity of the probe or primer towards the target sequence. For applications requiring high selectivity, relatively stringent conditions can be used, such as low salt and/or high temperature conditions, such as provided by a salt concentration of from about 0.02 M to about 0.15 M salt at temperatures of from about 50° C. to about 70° C. For applications requiring less selectivity, less stringent hybridization conditions can be used. For example, salt conditions from about 0.14 M to about 0.9M salt, at temperatures ranging form about 20° C. to about 55° C. The presence of a hybridized complex comprising the probe or primer and a complementary polynucleotide from the test sample indicates the presence of Pg or a Pg polynucleotide sequence in the sample.

The materials for use in a detection method of the invention can be present in a kit. A kit can comprise one or more elements used in the method. For example, a kit can contain one or more antibodies, antibody fragments, single-chain antibodies, polypeptides, or polynucleotides of the invention in one or more containers. The kit and container or containers are labeled with their contents and the kit includes instructions for use of the elements in the containers. The constituents of the kit can be present in, for example, liquid or lypholized form.

Methods of Treatment and Prevention

Diseases and symptoms in a subject caused by Pg can be treated and/or prevented in a subject by, for example, administration to or immunization of a subject with polynucleotides and/or polypeptides and/or aptamers of the invention.

Diseases caused by Pg include, for example, early-onset periodontitis including localized and generalized prepubertal periodontitis, localized and generalized juvenile periodontitis, and rapidly progressive or refractory adult periodontitis, endocarditis, thyroid gland abscesses, urinary tract infections, brain abscesses, vertebral osteomyelitis, and cardiovascular diseases.

A polypeptide, polynucleotide, antibody, antibody fragment, or single-chain antibody of the invention can be administered to a subject, for example, a mammal, such as a mouse, rabbit, guinea pig, macaque, baboon, chimpanzee, human, cow, sheep, pig, horse, dog, cat, or to animals such as chickens or ducks.

One embodiment of the invention provides a composition comprising an antibody, antibody fragment, single-chain antibody, polynucleotide or fragment thereof, polypeptide or fragment thereof and a pharmaceutically acceptable carrier.

One embodiment of the invention provides a composition for use in the treatment or prevention of periodontal diseases and symptoms in a subject, which comprises an amount, such as an immunologically effective amount, of a polypeptide of the invention (e.g., SEQ ID NOs:167-226, 228-261, and 263-354), polynucleotide of the invention, or an antibody, antibody fragment, or single-chain antibody or fragment thereof and one or more pharmaceutically acceptable carriers. Treatment is the reduction, amelioration, or elimination of one or more periodontal disease symptoms.

An immunologically effective amount is an amount sufficient to stimulate the immune system, directly or indirectly. This stimulation of the immune system can confer immunity against Pg-mediated diseases, such as periodontal diseases, or symptoms thereof. An effective amount is determined the severity of the disease, age, sex and weight of the patient, as well as the patient's general condition, and by other considerations known to the attending physician.

Compositions of the invention can be used to illicit immunity to periodontal diseases and symptoms. Administration of antibodies, antibody fragments, single-chain antibodies or aptamers of the invention to a subject can provide humoral immunity. This passive immunization provides substantially immediate protection. Active immunization can be achieved by administering polypeptides, polynucleotides and/or fragments thereof of the invention to a subject.

The invention also provides compositions for use in the treatment or prevention of one or more periodontal disease symptoms comprising a therapeutically effective amount of an antibody, antibody fragment, or single-chain antibody of the invention, polynucleotide, polypeptide, or aptamer of the invention optionally with one or more pharmaceutically acceptable carriers. Such compositions can be administered to a subject for the treatment or prevention of one or more periodontal disease symptoms. A therapeutically effective amount is an amount effective in preventing or alleviating the symptoms of a disease caused by Pg or in reducing the amount of Pg organisms in a subject.

The invention also provides compositions for use in treatment or prevention of periodontal disease symptoms in a subject, which comprises an immunologically effective amount of a polypeptide shown in SEQ ID NOs:167-226, 228-261, and 263-354 or fragments thereof and, optionally one or more pharmaceutically acceptable carriers. Optionally, an adjuvant can also be present in the composition, or can be administered before or after the composition. Such compositions can be administered to a subject for the treatment or prevention of one or more periodontal disease symptoms.

The administration of one or more polypeptides of the invention can result in production of anti-Pg antibodies, resulting in a reduction in and/or prevention of periodontal diseases and symptoms thereof.

Modifications can be made to a polypeptide of the invention to increase its immunogenicity. For example, a polypeptide can be conjugated or coupled with a carrier, e.g. a Cholera toxin B chain or monoclonal antibody. The polypeptide can be precipitated with aluminum salts or cross-linked with formaldehyde or other aldehydes. The polypeptide can be mixed with a physiologically acceptable diluent such as water, phosphate buffered saline, or saline. A composition of the invention can further comprise an adjuvant.

The invention additionally provides compositions for use in the treatment or prevention or one or more periodontal disease symptoms comprising an immunologically effective amount of one or more polynucleotides shown in SEQ ID NOs:1-166, 227, and 262, one or more polynucleotides that encode one or more polypeptides shown in SEQ ID NOs:167-226, 228-261, and 263-354, or fragments thereof and, optionally, one or more pharmaceutically acceptable carriers. Such compositions can be administered to a subject for the treatment or prevention of one or more periodontal disease symptoms.

In one embodiment of the invention various polynucleotide constructs, including polynucleotides of the invention and aptamers of the invention can be used as part of a gene therapy protocol to deliver polynucleotides of the invention to a subject. For example, expression vectors can be used for in vivo transfection and expression of a polypeptide.

Injection of a polynucleotide to a subject has the practical advantages of simplicity of construction and modification. Further, injection of a polynucleotide results in the synthesis of a polypeptide in the host. Thus, the polypeptide is presented to the host immune system with native post-translational modifications, structure, and conformation. A polynucleotide can be delivered to a subject as “naked DNA.”

Polypeptides or polynucleotides of the invention along with fragments thereof can be used to elicit an immune response in a host. An immunogenic polypeptide or polynucleotide is a polypeptide or polynucleotide of the invention that is capable of inducing an immune response in an animal. An immunogenic polypeptide or polynucleotide of the invention is particularly useful in sensitizing an immune system of an animal such that, as one result, an immune response is produced that ameliorates or prevents the effect of Pg infection. The elicitation of an immune response in animal model can be useful to determine, for example, optimal doses or administration routes. Elicitation of an immune response can also be used to treat, prevent, or ameliorate a disease or infection caused by Pg. An immune response includes humoral immune responses or cell mediated immune responses, or a combination thereof. An immune response can also comprise the promotion of a generalized host response, e.g., by promoting the production of defensins.

The generation of an antibody titer by an animal against Pg can be important in protection from infection and clearance of infection. Detection and/or quantification of antibody titers after delivery of a polypeptide or polynucleotide can be used to identify epitopes that are particularly effective at eliciting antibody titers. Epitopes responsible for a strong antibody response to Pg can be identified by eliciting antibodies directed against Pg polypeptides of different lengths. Antibodies elicited by a particular polypeptide epitope can then be tested using, for example, an ELISA assay to determine which polypeptides contain epitopes that are most effective at generating a strong response. Polypeptides or fusion proteins that contain these epitopes or polynucleotides encoding the epitopes can then be constructed and used to elicit a strong antibody response.

A pharmaceutically acceptable composition or formulation is in a form suitable for administration into a cell or subject. Suitable forms, in part, depend upon the use or the route of entry. Such forms should not prevent the composition or formulation from reaching a target cell or organ. For example, pharmacological compositions injected into the blood stream should be soluble. Other factors are known in the art, and include considerations such as toxicity and forms that prevent the composition or formulation from exerting its effect.

The present invention also includes pharmaceutically acceptable compositions prepared for storage or administration, which include the desired compounds in a pharmaceutically acceptable carrier, diluent, additive, excipient or adjuvant. By the terms “pharmaceutically acceptable carriers, diluents additives, excipients and adjuvants” is meant any inert, non-toxic material that can assist in the efficient delivery of the active ingredient. Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985) hereby incorporated by reference herein. For example, preservatives, stabilizers, dyes and flavoring agents can be provided. These include sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid. In addition, antioxidants and suspending agents can be used.

A carrier should not itself induce the production of antibodies harmful to the host. Such carriers include, but are not limited to, large, slowly metabolized, macromolecules, such as proteins, polysaccharides such as latex functionalized sepharose, agarose, cellulose, cellulose beads and the like, polylactic acids, polyglycolic acids, polymeric amino acids such as polyglutamic acid, polylysine, and the like, amino acid copolymers, peptoids, lipitoids, and inactive, avirulent virus particles or bacterial cells. Liposomes, hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesives can also be used as a carrier for a composition of the invention.

Pharmaceutically acceptable salts can also be used in compositions of the invention, for example, mineral salts such as hydrochlorides, hydrobromides, phosphates, or sulfates, as well as salts of organic acids such as acetates, proprionates, malonates, or benzoates. Especially useful protein substrates are serum albumins, keyhole limpet hemocyanin, immunoglobulin molecules, thyroglobulin, ovalbumin, tetanus toxoid, and other proteins well known to those of skill in the art. Compositions of the invention can also contain liquids or excipients, such as water, saline, phosphate buffered saline, Ringer's solution, Hank's solution, glucose, glycerol, dextrose, malodextrin, ethanol, or the like, singly or in combination, as well as substances such as wetting agents, emulsifying agents, tonicity adjusting agents, detergent, or pH buffering agents. Additional active agents, such as bacteriocidal agents can also be used. Polypeptides, polynucleotides, antibodies, single-chain antibodies and fragments thereof and aptamers of the invention can be delivered by numerous delivery routes.

The pharmaceutically acceptable formulations can be locally delivered by, for example, direct injection or by use of an infusion pump. Direct injection, such as subcutaneous, intramuscular, or intradermal injection, can take place using standard needle and syringe methodologies, or by needle-free technologies such as those described in Conry et al., 1999, Clin. Cancer Res., 5, 2330-2337 and Barry et al., International PCT Publication No. WO 99/31262.

A polynucleotide can be directly administered, for example by injection, to a subject and expressed as a protein. The DNA or RNA can be either associated with a delivery vehicle (e.g., viruses, bacteria, liposomes, and gold beads) or naked (free from association with transfection-facilitating proteins, viral particles, liposomal formulations, charged lipids and calcium phosphate precipitating). The polynucleotide can optionally include a promoter, e.g., a viral promoter. The polypeptide encoded by the polynucleotide is produced in the subject, resulting in the generation of an immune response. Methods of delivery of polynucleotides to a host cell are described in Akhtar et al., 1992, Trends Cell Bio., 2, 139; Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, 1995, Maurer et al., 1999, Mol. Membr. Biol., 16, 129-140; Hofland and Huang, 1999, Handb. Exp. Pharmacol., 137, 165-192; and Lee et al., 2000, ACS Symp. Ser., 752, 184-192. Polynucleotides can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other delivery vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (O'Hare and Normand, International PCT Publication No. WO 00/53722). Alternatively, the polynucleotide/vehicle combination is locally delivered by direct injection or by use of an infusion pump. Direct injection of the polynucleotide molecules of the invention, whether subcutaneous, intramuscular, or intradermal, can take place using standard needle and syringe methodologies, or by needle-free technologies such as those described in Conry et al., 1999, Clin. Cancer Res., 5, 2330-2337 and Barry et al., International PCT Publication No. WO 99/31262. Osmotic pump (see Chun et al., 1998, Neuroscience Letters, 257, 135-138, D'Aldin et al., 1998, Mol. Brain Research, 55, 151-164, Dryden et al., 1998, J. Endocrinol., 157, 169-175, Ghirnikar et al., 1998, Neuroscience Letters, 247, 21-24) or direct infusion (Broaddus et al., 1997, Neurosurg. Focus, 3, article 4) techniques can also be used. Other routes of delivery include, but are not limited to oral (tablet or pill form) and/or intrathecal delivery (Gold, 1997, Neuroscience, 76, 1153-1158).

Attenuated viruses or bacteria can be used in the invention by genetically-modifying an attenuated virus or bacteria so that is expresses a polypeptide of the invention. This modified vector can then be delivered to a subject, resulting in the in vivo production of the polynucleotide such that an immune response is generated in the subject. Polynucleotide molecules can be inserted into microorganisms by standard methods known in the art. See e.g., U.S. Pat. No. 5,866,136 and U.S. Pat. No. 6,025,164.

A polynucleotide of the invention can also be included in the genome of a plant, so that a polypeptide of the invention is produced by the plant. The genetically-modified plant is then consumed by a subject, resulting in the ingestion of a polypeptide of the invention and the generation of an immune response. Edible plant vaccines are described in, e.g., WO 99/54452. An edible vaccine is administered orally, e.g., consuming a genetically-modified plant. The genetically-modified plant can be in the form of a plant part, extract, juice, liquid, powder, or tablet. The edible vaccine can also be administered via an intranasal route.

Compositions of the invention can be delivered to a subject by systemic administration. Systemic administration is in vivo systemic absorption or accumulation of drugs in the blood stream followed by distribution throughout the entire body. Administration routes that can lead to systemic absorption include, without limitation: intravenous, subcutaneous, intraperitoneal, inhalation, transdermal, oral, intrapulmonary and intramuscular.

The compositions of the invention and formulations thereof can be administered orally, topically, parenterally, mucosal, by inhalation or spray, or rectally (suppository) in dosage unit formulations. The term parenteral as used herein includes percutaneous, subcutaneous, intravascular (e.g., intravenous), intradermal, intramuscular, intrapulmonary, intraperiotoneal, or intrathecal injection or infusion techniques and the like. A pharmaceutically acceptable formulation of the invention can be delivered to a subject by a liposome delivery mechanism. Standard protocols for formation of liposomes can be followed. A combination of administration methods can also be used.

Polypeptides, polynucleotides, or antibodies, or a combination thereof can be administered either to an animal that is not infected with Pg or can be administered to a Pg-infected animal.

If desired, co-stimulatory molecules, which improve immunogen presentation to lymphocytes, such as B7-1 or B7-2, or cytokines such as MIP1α, GM-CSF, IL-2, and IL-12, can be included in a composition of the invention. Optionally, adjuvants can also be included in a composition. Adjuvants are substances that can be used to nonspecifically augment a specific immune response. Generally, an adjuvant and a polypeptide of the invention are mixed prior to presentation to the immune system, or presented separately, but are presented into the same site of the animal. Adjuvants can include, for example, oil adjuvants (e.g. Freund's complete and incomplete adjuvants) mineral salts (e.g. Alk(SO₄)₂; AlNa(SO₄)₂, AlNH₄(SO₄), Silica, Alum, Al(OH)₃, and Ca₃(PO₄)₂), polynucleotides (i.e. Polyic and Poly AU acids), and certain natural substances (e.g. wax D from Mycobacterium tuberculosis, as well as substances found in Corynebacterium parvum, Bordetella pertussis and members of the genus Brucella. Adjuvants which can be used include, but are not limited to MF59-0, aluminum hydroxide, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637), referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP 19835A, referred to as MTP-PE), and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/TWEEN 80 emulsion. Additional descriptions of antigenic protein-adjuvant combinations are described in WO 99/54452 and WO 99/49890.

An immunologically effective amount of a polypeptide, polynucleotide, antibody, or antibody fragment, or single-chain antibody of the invention is an amount that is delivered to a subject, either in a single dose or as part of a series, which is effective to stimulate the immune system, directly or indirectly. This amount varies depending upon the health and physical condition of the individual to be treated, the taxonomic group of individual to be treated, the capacity of the individual's immune system to synthesize antibodies, the degree of protection desired, the formulation of the vaccine, the assessment of the medical situation, and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials.

The pharmaceutical compositions can be in a form suitable for oral use, for example, as tablets, troches, lozenges, aqueous or oily suspensions, dispersible powders or granules, emulsion, hard or soft capsules, syrups, dentrifices, mouthwashes, gels or elixirs. Compositions intended for oral use can be prepared according to any method known to the art for the manufacture of pharmaceutical compositions and such compositions can contain one or more such sweetening agents, flavoring agents, coloring agents or preservative agents in order to provide pharmaceutically elegant and palatable preparations. Tablets contain the active ingredient or ingredients in admixture with non-toxic pharmaceutically acceptable excipients that are suitable for the manufacture of tablets. These excipients can be, for example, inert diluents; such as calcium carbonate, sodium carbonate, lactose, calcium phosphate or sodium phosphate; granulating and disintegrating agents, for example, corn starch, or alginic acid; binding agents, for example starch, gelatin or acacia; and lubricating agents, for example magnesium stearate, stearic acid or talc. The tablets can be uncoated or they can be coated by known techniques. In some cases such coatings can be prepared by known techniques to delay disintegration and absorption in the gastrointestinal tract and thereby provide a sustained action over a longer period. For example, a time delay material such as glyceryl monosterate or glyceryl distearate can be employed.

Formulations for oral use can also be presented as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent, for example, calcium carbonate, calcium phosphate or kaolin, or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium, for example peanut oil, liquid paraffin or olive oil.

Aqueous suspensions contain the active materials in a mixture with excipients suitable for the manufacture of aqueous suspensions. Such excipients are suspending agents, for example sodium carboxymethylcellulose, methylcellulose, hydropropyl-methylcellulose, sodium alginate, polyvinylpyrrolidone, gum tragacanth and gum acacia; dispersing or wetting agents can be a naturally-occurring phosphatide, for example, lecithin, or condensation products of an alkylene oxide with fatty acids, for example polyoxyethylene stearate, or condensation products of ethylene oxide with long chain aliphatic alcohols, for example heptadecaethyleneoxycetanol, or condensation products of ethylene oxide with partial esters derived from fatty acids and a hexitol such as polyoxyethylene sorbitol monooleate, or condensation products of ethylene oxide with partial esters derived from fatty acids and hexitol anhydrides, for example polyethylene sorbitan monooleate. The aqueous suspensions can also contain one or more preservatives, for example ethyl, or n-propyl p-hydroxybenzoate, one or more coloring agents, one or more flavoring agents, and one or more sweetening agents, such as sucrose or saccharin.

Oily suspensions can be formulated by suspending the active ingredients in a vegetable oil, for example arachis oil, olive oil, sesame oil or coconut oil, or in a mineral oil such as liquid paraffin. The oily suspensions can contain a thickening agent, for example beeswax, hard paraffin or cetyl alcohol. Sweetening agents and flavoring agents can be added to provide palatable oral preparations. These compositions can be preserved by the addition of an anti-oxidant such as ascorbic acid.

Dispersible powders and granules suitable for preparation of an aqueous suspension by the addition of water provide the active ingredient in admixture with a dispersing or wetting agent, suspending agent and one or more preservatives. Suitable dispersing or wetting agents or suspending agents are exemplified by those already mentioned above. Additional excipients, for example sweetening, flavoring and coloring agents, can also be present.

Pharmaceutical compositions of the invention can also be in the form of oil-in-water emulsions. The oily phase can be a vegetable oil or a mineral oil or mixtures of these. Suitable emulsifying agents can be naturally-occurring gums, for example gum acacia or gum tragacanth, naturally-occurring phosphatides, for example soy bean, lecithin, and esters or partial esters derived from fatty acids and hexitol, anhydrides, for example sorbitan monooleate, and condensation products of the said partial esters with ethylene oxide, for example polyoxyethylene sorbitan monooleate. The emulsions can also contain sweetening and flavoring agents.

Syrups and elixirs can be formulated with sweetening agents, for example glycerol, propylene glycol, sorbitol, glucose or sucrose. Such formulations can also contain a demulcent, a preservative and flavoring and coloring agents. The pharmaceutically acceptable compositions can be in the form of a sterile injectable aqueous or oleaginous suspension. This suspension can be formulated according to the known art using those suitable dispersing or wetting agents and suspending agents that have been mentioned above. The sterile injectable preparation can also be a sterile injectable solution or suspension in a non-toxic parentally acceptable diluent or solvent, for example as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid find use in the preparation of injectables.

The compositions of the invention can also be administered in the form of suppositories, e.g., for rectal administration of the drugs. These compositions can be prepared by mixing the drug with a suitable non-irritating excipient that is solid at ordinary temperatures but liquid at the rectal temperature and will therefore melt in the rectum to release the drug. Such materials include cocoa butter and polyethylene glycols.

Compositions can be administered parenterally in a sterile medium. The drug, depending on the vehicle and concentration used, can either be suspended or dissolved in the vehicle. Advantageously, adjuvants such as local anesthetics, preservatives and buffering agents can be dissolved in the vehicle.

For administration to non-human animals, the composition can also be added to the animal feed or drinking water. It can be convenient to formulate the animal feed and drinking water compositions so that the animal takes in an appropriate quantity of the composition along with its diet. It can also be convenient to present the composition as a premix for addition to the feed or drinking water.

A pharmaceutically effective dose is that dose required to treat or prevent one or more Pg-induced disease symptoms in a subject. The pharmaceutically effective dose depends on the type of disease, the composition used, the route of administration, the type of subject being treated, the physical characteristics of the specific subject under consideration, age, gender, general condition of the subject, diet, concurrent medication, and other factors that those skilled in the medical arts will recognize. An effective amount of the composition of the invention can be readily determined using only routine experimentation.

A composition of the invention is administered in a manner compatible with the particular composition used and in an amount that is effective to elicit an immune response as detected by, for example, an ELISA. Antibodies and polypeptides can be administered at a daily dose of about 0.05 mg/kg to about 100 mg/kg. In one embodiment of the invention antibodies and polypeptides can be are administered at a daily dose of about 20 to about 100 mg/kg. In another embodiment antibodies and polypeptides can be administered to a subject at a dose of, for example, from about 0.05 mg/kg to about 5 mg/kg. A polypeptide of the invention can be administered at a dose of, for example. 0.01, 0.05, 0.5, 0.75, 1.0, 1.5, 2.0, 2.5, 5 or 10 mg/kg.

Administration of compositions of the invention can elicit an immune response in the animal that lasts for at least 1 week, 1 month, 3 months, 6 months, 1 year, or longer. Optionally, an immune response can be maintained in an animal by providing one or more booster administrations of the compositions of the invention at 1 month, 3 months, 6 months, 1 year, or more after the primary administration. If desired, co-stimulatory molecules or adjuvants can also be provided before, after, or together with the compositions.

All patents, patent applications, and other scientific or technical writings referred to anywhere herein are incorporated by reference in their entirety. The invention illustratively described herein suitably can be practiced in the absence of any element or elements, limitation or limitations that are not specifically disclosed herein. Thus, for example, in each instance herein any of the terms “comprising”, “consisting essentially of”, and “consisting of” may be replaced with either of the other two terms. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by embodiments, optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the description and the appended claims.

In addition, where features or aspects of the invention are described in terms of Markush groups or other grouping of alternatives, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group or other group.

TABLE 2 SEQ SEQ ID NO Clone Name of Homologous ID NO (amino Number Locus ORF Function (DNA) acid) SW 2 1711 alpha-1,2-mannosidase Biosynthesis and 1 167 family protein degradation of surface polysaccharides and lipopolysaccharides SW 4 0047 cell division protein, Cell division 2 168 FtsH, putative SW 5 1282 conserved hypothetical Unknown function 3 169 SW 5 1283 conserved hypothetical Unknown function 3 170 SW 6 1845, ISPg1 transposase Transposon functions 4 et. al. SW 7 0968 Mrr restriction system DNA metabolism; 5 340 protein Restriction/modification SW 9 1885 polyphosphate kinase Central intermediary 6 171 metabolism: Phosphorus compounds SW 12 0082 hypothetical Unknown function 7 172 SW 13 0310 nitroreductase family Unknown function 8 173 protein SW 15 1908 hypothetical Unknown function 9 174 SW 18 1413 hypothetical Unknown function 10 175 SW 34 1844 lysine-specific cysteine Degradation of proteins, 11 176 proteinase, authentic peptides, and frameshift glycopeptides SW 36 2071 conserved domain Unknown function 12 177 protein SW 36 2072 UvrD/REP helicase Unknown function 12 178 domain protein (Repair-putative) SW 37 1888 conserved hypothetical Unknown function 13 179 SW 37 1889 hypothetical Unknown function 13 180 SW 41 0590 ISPg5 transposase Transposon functions 14 181 et al ORF1 SW 43 2071 conserved domain Unknown function 15 182 protein SW 43 2072 UvrD/REP helicase Unknown function 15 183 domain protein (Repair-putative) SW 47 2047 helicase, putative Enzymes of unknown 16 184 specificity SW 54 2216 hypothetical Unknown function 17 185 SW 56 2024 arginine-specific Degradation of proteins, 18 186 protease ArgI peptides, and polyprotein glycopeptides SW 57 2056 transposase ISPg2- Transposon functions 19 187 related, truncation SW 60 1545 superoxide dismutase, Detoxification 20 188 Fe—Mn SW 60 1546 hypothetical Unknown function 20 189 SW 61 0062 TPR domain protein Unknown function 21 190 SW 62 0944 ISPg 1 transposase Transposon functions 22 191 et al SW 64 1844 lysine-specific cysteine Degradation of proteins, 23 192 proteinase, authentic peptides, and frameshift glycopeptides SW 69 0012 L-threonine-O-3- Biosynthesis of 24 193 phosphate cofactors, prosthetic decarboxylase, putative groups, and carriers: Heme, porphyrin, and cobalamin SW 70 0766 polyribonucleotide Degradation of RNA 25 194 nucleotidyltransferase SW 78 2125 transcriptional Regulatory DNA 26 195 regulator, AraC family interactions SW 80 0383 membrane-associated Degradation of proteins, 27 196 zinc metalloprotease, peptides, and putative glycopeptides SW 80 0384 MutS2 family protein DNA mismatch binding 27 197 protein of unknown cellular function SW 87 0293 secretion activator Protein and peptide 28 198 protein, putative secretion and trafficking SW 88 0383 membrane-associated Degradation of proteins, 29 199 zinc metalloprotease, peptides, and putative glycopeptides SW 88 0384 MutS2 family protein DNA mismatch binding 29 200 protein of unknown cellular function SW 89 0968 Mrr restriction system DNA metabolism; 30 341 protein Restriction/modification SW 94 1788 cysteine peptidase, Degradation of proteins, 31 201 putative peptides, and glycopeptides SW 99 1039 integral membrane Cell envelope 32 202 protein SW 100 0293 secretion activator Protein and peptide 33 203 protein, putative secretion and trafficking SW 101 0590 ISPg5 transposase Transposon functions 34 204 et al ORF1 SW 107 2125 transcriptional Regulatory DNA 35 205 regulator, AraC family interactions SW 112 0525 CTP synthase Pyrimidine 36 206 ribonucleotide biosynthesis SW 113 0679 outer membrane efflux Transport and binding 37 207 protein proteins: Unknown substrate SW 114 1021 hypothetical Unknown function 38 208 SW 114 1022 hypothetical Unknown function 38 209 SW 115 2024 arginine-specific Degradation of proteins, 39 210 protease ArgI peptides, and polyprotein glycopeptides SW 115 1844 lysine-specific cysteine Degradation of proteins, 39 211 proteinase, authentic peptides, and frameshift glycopeptides SW 119 1974 hypothetical; P.g. 381 Unknown function 40 212 HagB & PgiM SW 120 1334 band7/Mec-2 family Unknown function 41 213 protein SW 125 1880 glycosyl transferase, Biosynthesis and 42 214 group 2 family protein degradation of surface polysaccharides and lipopolysaccharides SW 127 43 SW 129 2125 transcriptional Regulatory DNA 44 215 regulator, AraC family interactions SW 134 45 SW 135 2115 protease PrtT, Degradation of proteins, 46 degenerate peptides, and glycopeptides SW 139 47 SW 140 0150 conserved hypothetical Unknown function 48 216 TIGR01125 SW 141 0483 kinase, putative Unknown function 49 217 SW 141 0484 hypothetical Unknown function 49 218 SW 142 2171 D-isomer specific 2- Unknown function 50 219 hydroxyacid dehydogenase family protein SW 144 1680 ABC transporter, ATP- Transport and binding 51 binding protein, proteins: Unknown authentic frameshift substrate SW 144 1681 glycogen debranching Unknown function 51 220 enzyme-related protein SW 150 0968 Mrr restriction system DNA metabolism; 52 342 protein Restriction/modification SW 151 2024 arginine-specific Degradation of proteins, 53 221 protease ArgI peptides, and polyprotein glycopeptides SW 151 1844 lysine-specific cysteine Degradation of proteins, 53 222 proteinase, authentic peptides, and frameshift glycopeptides SW 153 0861 helicase, SNF2/RAD4 DNA replication, 54 223 family recombination, and repair SW 153 0862 type IIS restriction DNA replication, 54 224 endonuclease, putative recombination, and repair SW 159 0451 CBS domain protein Unknown function 55 343 SW 159 0452 CBS domain protein Unknown function 55 344 SW 162 0548 pyruvate Energy metabolism: 56 225 ferredoxin/flavodoxin Electron transport oxidoreductase family protein SW 165 0668 TonB-dependent Transport and binding 57 226 receptor proteins: Cations SW 165 partial clone 227 SW 166 2174 hypothetical, P.g. W50 Unknown function 58 228 28 kDa OMP; Omp28 SW 166 2175 conserved hypothetical Unknown function 58 229 SW 167 0712 hypothetical Unknown function 59 230 SW 169 0530 carbamoyl-phosphate Pyrimidine 60 231 synthase, large subunit ribonucleotide biosynthesis SW 173 61 SW 174 0502 SsrA-binding protein Protein synthesis 62 232 SW 182 0451 CBS domain protein Unknown function 63 345 SW 182 0452 CBS domain protein Unknown function 63 346 SW 185 0285 hypothetical Unknown function 64 233 SW 200 1812 2-oxoglutarate Energy metabolism: 65 234 oxidoreductase, alpha Fermentation subunit SW 203 0287 hypothetical Unknown function 66 235 SW 203 0288 lipoprotein Surface, Cell envelope 66 236 SW 208 1591 conserved hypothetical Unknown function 67 237 SW 210 68 SW 214 0293 secretion activator Protein and peptide 69 238 protein, putative secretion and trafficking SW 223 2024 arginine-specific Degradation of proteins, 70 239 protease ArgI peptides, and polyprotein glycopeptides SW 248 2165 glycyl-tRNA Protein synthesis: tRNA 71 240 synthetase aminoacylation SW 248 2166 hypothetical Unknown function 71 241 SW 254 0114 hypothetical Unknown function 72 242 SW 259 0228 DdaH family protein Unknown function 73 243 SW 263 0292 chromate transport Transport and binding 74 protein, authentic proteins: Anions frameshift SW 263 0293 secretion activator Protein and peptide 74 244 protein, putative secretion and trafficking SW 266 0026 hypothetical Unknown function 75 245 SW 267 2125 transcriptional Regulatory DNA 76 246 regulator, AraC family interactions SW 278 1889 hypothetical Unknown function 77 247 SW 279 1474 conjugative transport Plasmid functions 78 248 protein TraO SW 282 1498 hypothetical Unknown function 79 249 SW 286 0293 secretion activator Protein and peptide 80 250 protein, putative secretion and trafficking SW 287 0324 histidine ammonia- Energy metabolism: 81 251 lyase Amino acids and amines SW 287 0325 conserved hypothetical Unknown function 81 252 SW 290 82 SW 300 1696 type II DNA Restriction/modification 83 253 modification methyltransferase, putative SW 300 1697 type II restriction Restriction/modification 83 254 endonuclease, putative SW 300 2216 hypothetical Unknown function 83 255 SW 301 84 SW 302 0383 membrane-associated Degradation of proteins, 85 256 zinc metalloprotease, peptides, and putative glycopeptides SW 302 0384 MutS2 family protein DNA mismatch binding 85 257 protein of unknown cellular function SW 303 0867 hypothetical Unknown function 86 347 SW 303 0868 mobilization protein Plasmid functions 86 258 SW 304 0345 hypothetical, M. avium Unknown function 87 259 23S ribosomal RNA gene SW 311 2082 POT family protein Transport and binding: 88 260 Amino acids, peptides and amines SW 312 0668 TonB-dependent Transport and binding 89 261 receptor proteins: Cations SW 312 partial clone 262 SW 314 1775 grpE protein Protein folding and 90 263 stabilization SW 316 0324 histidine ammonia- Energy metabolism: 91 264 lyase Amino acids and amines SW 316 0325 conserved hypothetical Unknown function 91 265 SW 320 2216 hypothetical Unknown function 92 266 SW 325 2216 hypothetical Unknown function 93 267 SW 327 0463 folylpolyglutamate Biosynthesis of 94 268 synthase cofactors, prosthetic groups, and carriers SW 330 0708 peptidyl-prolyl cis- Protein folding and 95 269 trans isomerase, stabilization FKBP-type, putative SW 330 0709 peptidyl-prolyl cis- Protein folding and 95 270 trans isomerase, FkpA, stabilization FKBP-type SW 331 1033 conserved hypothetical 96 348 protein SW 331 1034 ABC transporter ATP-binding protein, 96 349 Transport and binding proteins SW 333 2216 hypothetical Unknown function 97 271 SW 335 2086 hypothetical Unknown function 98 272 SW 336 2086 hypothetical Unknown function 99 273 SW 337 100 SW 339 0048 conserved hypothetical Unknown function 101 274 SW 340 0048 conserved hypothetical Unknown function 102 275 SW 344 2216 hypothetical Unknown function 103 276 SW 345 2216 hypothetical 104 350 SW 347 ABC transporter, Transport and binding 105 277 permease protein, proteins: Unknown putative substrate SW 348 0048 conserved hypothetical Unknown function 106 278 SW 351 2131 60 kDa protein Unknown function 107 279 SW 353 2197 conserved hypothetical Unknown function 108 280 SW 354 2216 hypothetical Unknown function 109 281 SW 355 1242 replicative DNA DNA replication, 110 282 helicase recombination, and repair SW 357 0531 glutamine-dependent Pyridine nucleotides 111 283 NAD+ synthetase SW 362 2066 hypothetical Unknown function 112 284 SW 363 0181 immunoreactive 32 kDa Unknown function 113 285 antigen PG49 SW 365 2008 hypothetical, hypo. Unknown function 114 286 tonB linked OMR PG35; PG W50 SW 370 0868 mobilization protein Plasmid functions 115 287 SW 372 0277 ISPg2 transposase Transposon functions 116 288 et al SW 377 1111 conserved hypothetical, Unknown function 117 auth. pt. mut., B. uniformis insertion seq. NBU1 SW 380 0104 DNA topoisomerase III DNA replication, 118 289 recombination, and repair SW 383 0810 hypothetical Unknown function 119 290 SW 383 0811 Holliday junction DNA DNA replication, 119 291 helicase RuvA recombination, and repair SW 384 2094 conserved domain Unknown function 120 292 protein SW 385 0095 DNA mismatch repair Cell division 121 293 protein MutS SW 386 2216 hypothetical Unknown function 122 294 SW 397 0867 hypothetical Unknown function 123 351 SW 397 0868 mobilization protein Plasmid functions 123 295 SW 412 0451 CBS domain protein Unknown function 124 352 SW 412 0452 CBS domain protein Unknown function 124 353 SW 413 1391 hypothetical Unknown function 125 296 SW 414 0048 conserved hypothetical Unknown function 126 297 SW 421 2086 hypothetical Unknown function 127 298 SW 423 1988 hypothetical Unknown function 128 299 SW 423 1989 hypothetical Unknown function 128 300 SW 423 1990 hypothetical, Y. pestis Unknown function 128 301 put. Virulence factor SW 424 2131 60 kDa protein Unknown function 129 302 SW 444 1977 hypothetical, Unknown function 130 303 pristinomycin biosynthesis SW 447 2197 conserved hypothetical Unknown function 131 304 SW 448 2150 LysM domain protein Unknown function 132 305 SW 448 2151 hypothetical, P.G. Unknown function 132 306 ATCC33277 dnaK operon genes SW 455 497 5′- 133 354 methylthioadenosine/S- adenosylhomocysteine nucleosidase SW 459 1417 fumarate hydratase Energy metabolism: 134 307 class I, anaerobic Anaerobic SW 463 1331 NAD(P) Energy metabolism: 135 transhydrogenase Electron transport alpha-subunit, authentic frameshift SW 463 1332 NAD(P) Energy metabolism: 135 308 transhydrogenase beta- Electron transport subunit SW 468 1947 TPR domain protein Unknown function 136 309 SW 37, 1889 hypothetical Unknown function 278 SW 41, 0590 ISPg5 transposase Transposon functions 101 et al ORF1 SW 165, 0668 TonB-dependent Transport and binding 312 receptor proteins: Cations SW 287, 0324 histidine ammonialyase Energy metabolism: 316 Amino acids and amines SW 287, 0325 conserved hypothetical Unknown function 316 SW 351, 2131 60 kDa protein Unknown function 424 SW 353, 2197 conserved hypothetical Unknown function 447 SW 303, 0868 mobilization protein Plasmid functions 370, 397 SW 2086 hypothetical Unknown function 335, 336, 421 SW 56, 2024 arginine-specific Degradation of proteins, 115, protease ArgI peptides, and 151, 223 polyprotein glycopeptides SW 78, 2125 transcriptional Regulatory DNA 107, regulator, AraC family interactions 129, 267 SW 339, 0048 conserved hypothetical Unknown function 340, 348, 414 SW 87, 0293 secretion activator Protein and peptide 100, protein, putative secretion and trafficking 214, 263, 286 SW 34, 1844 lysine-specific cysteine Degradation of proteins, 64, 115, proteinase, authentic peptides, and 151 frameshift glycopeptides SW 36, 2071 conserved domain Unknown function 43 protein SW 36, 2072 UvrD/REP helicase Unknown function 43 domain protein (Repair-putative) SW 54, 2216 hypothetical Unknown function 320, 325, 333, 344, 300, 354, 386 SW 80, 0383 membrane-associated Degradation of proteins, 88, 302 zinc metalloprotease, peptides, and putative glycopeptides SW 80, 0384 MutS2 family protein DNA mismatch binding 88, 302 protein of unknown cellular function YHS 1/p 1082 Phosphotransacetylase Energy metabolism: 137 310 Fermentation YHS 1/t 1081 Acetate kinase Energy metabolism: 138 311 Fermentation YHS 0333 membrane protein, Cell envelope 139 312 10/p putative YHS 140 10/t YHS 1774 transcription-repair DNA replication, 141 313 15/p coupling factor recombination, and repair YHS 142 15/t YHS 2204 hypothetical protein Hypothetical proteins 143 314 18/p YHS 144 18/t YHS 1017 pyruvate phosphate Energy metabolism 145 315 23/p dikinase YHS 1018 hypothetical protein Hypothetical proteins 145 316 23/p YHS 146 23/t YHS 0339 hypothetical protein Hypothetical proteins 147 317 28/p YHS 148 28/t YHS 1896 S-adenosylmethionine Central intermediary 149 318 32/p synthase metabolism YHS 150 32/t YHS 0196 peptidase, M16 family Degradation of proteins, 151 319 34/p peptides, and glycopeptides YHS 152 34/t YHS 0365 3′-5′ exonuclease Unknown function 153 320 40/p domain protein YHS 0064 heavy metal efflux Transport and binding 153 321 40/p pump, CzcA family proteins YHS 0364 conserved hypothetical Hypothetical proteins 153 322 40/p protein YHS 2076 hypothetical protein Hypothetical proteins 154 323 40/t YHS 1697 type II restriction DNA metabolism: 155 324 46/p endonuclease, putative Restriction/modification YHS 1214 hypothetical protein Hypothetical proteins 156 325 46/t YHS None Unknown function 157 48/p YHS 0680 conserved hypothetical Hypothetical proteins 158 326 48/t protein YHS 0701 cobinamide Biosynthesis of 159 327 52/p kinase/cobinamide cofactors, prosthetic phosphate groups, and carriers guanylyltransferase YHS 0700 hypothetical protein Hypothetical proteins 159 328 52/p YHS 1880 glycosyl transferase, Biosynthesis and 160 329 52/t group 2 family protein degradation of surface polysaccharides and lipopolysaccharides YHS 1881 hypothetical protein Hypothetical proteins 160 330 52/t YHS 0217 hypothetical protein Hypothetical proteins 161 331 53/p YHS 0386 site-specific DNA replication, 162 332 53/t recombinase, phage recombination, and integrase family/ repair ribosomal subunit interface protein YHS 1436 ATPase, putative Central intermediary 163 333 55/p metabolism YHS 1435 integrase Central intermediary 164 334 55/t metabolism YHS 1656 methylmalonyl-CoA Energy metabolism: 165 335 56/p mutase, small subunit Fermentation YHS 1413 hypothetical protein Hypothetical proteins 165 336 56/p YHS 1168 hypothetical protein Hypothetical proteins 165 337 56/p YHS 1925 ribosomal protein S14 Ribosomal proteins: 165 338 56/p synthesis and modification YHS 2040 hypothetical protein Hypothetical proteins 165 339 56/p YHS 166 56/t Sequences with 85% homology or higher were chosen. In all cases, homologous sequences are listed according to degree of homology in descending order for each clone. For sequencing, the T7 promoter and terminator primers were used. Sequences arising from both primers were blasted against the TIGR P. gingivalis database. When a particular homology showed up from sequence derived from both primers, only the one from the promoter primer was reported here. 

1. A method of detecting the presence of antibodies specific for Porphyromonas gingivalis in a test sample comprising: contacting the test sample with isolated polypeptides comprising SEQ ID NO:207 under conditions that allow formation of immunocomplexes between the antibodies and the polypeptides, wherein the polypeptides specifically bind antibodies specific for Porphyromonas gingivalis; and detecting the immunocomplexes between the antibodies and the polypeptides, wherein detection of the immunocomplexes between the antibodies and the polypeptides indicates the presence of antibodies specific for Porphyromonas gingivalis in the test sample.
 2. The method of claim 1, wherein the isolated polypeptides comprise a fusion protein comprising SEQ ID NO:207 and a heterologous polypeptide.
 3. The method of claim 1, wherein the amount of immunocomplexes is determined.
 4. The method of claim 1, wherein the isolated polypeptides are labeled.
 5. The method of claim 1, wherein the isolated polypeptides are unlabeled.
 6. The method of claim 1, wherein detecting the immunocomplexes is done by western blot analysis, enzyme-linked immunosorbant assay, or a radioimmunoassay.
 7. A method for detecting the presence of antibodies specific for Porphyromonas gingivalis in a subject comprising: (a) obtaining a biological sample from the subject; (b) contacting the biological sample with isolated polypeptides comprising SEQ ID NO:207 under conditions that allow formation of immunocomplexes between the isolated polypeptides and the antibodies specific for Porphyromonas gingivalis present in the biological sample; (c) detecting the amount of immunocomplexes formed in step (b); and (d) comparing the amount of immunocomplexes detected in step (c) to a control sample; wherein a higher amount of immunocomplexes in the biological sample than the control sample indicates the presence of antibodies specific for Porphyromonas gingivalis in the subject.
 8. The method of claim 7, wherein the isolated polypeptides comprise a fusion protein comprising SEQ ID NO:207 and a heterologous polypeptide.
 9. The method of claim 7, wherein the isolated polypeptides are labeled.
 10. The method of claim 7, wherein the isolated polypeptides are unlabeled.
 11. The method of claim 7, wherein detecting the immunocomplexes is done by western blot analysis, enzyme-linked immunosorbant assay, or a radioimmunoassay. 